MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences
<p>Abstract</p> <p>Background</p> <p>Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study r...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-02-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/10/72 |
| _version_ | 1811330073247088640 |
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| author | Roch Philippe Bovo Giuseppe De Nardi Barbara Varotto Laura Bernante Filippo De Pittà Cristiano Venier Paola Novoa Beatriz Figueras Antonio Pallavicini Alberto Lanfranchi Gerolamo |
| author_facet | Roch Philippe Bovo Giuseppe De Nardi Barbara Varotto Laura Bernante Filippo De Pittà Cristiano Venier Paola Novoa Beatriz Figueras Antonio Pallavicini Alberto Lanfranchi Gerolamo |
| author_sort | Roch Philippe |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of <it>Mytilus galloprovincialis </it>(the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.</p> <p>Results</p> <p>We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant <it>M. galloprovincialis </it>sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database <url>http://mussel.cribi.unipd.it</url>.</p> <p>Conclusion</p> <p>We defined the first species-specific catalogue of <it>M. galloprovincialis </it>ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.</p> |
| first_indexed | 2024-04-13T15:55:10Z |
| format | Article |
| id | doaj.art-56a554e6c867426aa9aa8cd3ed123e2d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T15:55:10Z |
| publishDate | 2009-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-56a554e6c867426aa9aa8cd3ed123e2d2022-12-22T02:40:42ZengBMCBMC Genomics1471-21642009-02-011017210.1186/1471-2164-10-72MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequencesRoch PhilippeBovo GiuseppeDe Nardi BarbaraVarotto LauraBernante FilippoDe Pittà CristianoVenier PaolaNovoa BeatrizFigueras AntonioPallavicini AlbertoLanfranchi Gerolamo<p>Abstract</p> <p>Background</p> <p>Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of <it>Mytilus galloprovincialis </it>(the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria.</p> <p>Results</p> <p>We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant <it>M. galloprovincialis </it>sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database <url>http://mussel.cribi.unipd.it</url>.</p> <p>Conclusion</p> <p>We defined the first species-specific catalogue of <it>M. galloprovincialis </it>ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels.</p>http://www.biomedcentral.com/1471-2164/10/72 |
| spellingShingle | Roch Philippe Bovo Giuseppe De Nardi Barbara Varotto Laura Bernante Filippo De Pittà Cristiano Venier Paola Novoa Beatriz Figueras Antonio Pallavicini Alberto Lanfranchi Gerolamo MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences BMC Genomics |
| title | MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences |
| title_full | MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences |
| title_fullStr | MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences |
| title_full_unstemmed | MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences |
| title_short | MytiBase: a knowledgebase of mussel (<it>M. galloprovincialis</it>) transcribed sequences |
| title_sort | mytibase a knowledgebase of mussel it m galloprovincialis it transcribed sequences |
| url | http://www.biomedcentral.com/1471-2164/10/72 |
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